for (@spliceout) {  
    s/\s+$//;  
}
##</code><code>##

#!/usr/bin/perl -w
use strict;

my $inputfile1 = $ARGV[0];
open (FILE1, $inputfile1) or die "Uh oh.. unable to find file $inputfile1"; ##Opens input file


my @file1 = <FILE1>; #loads inputfile1 data into array
close FILE1;


my @matches;
foreach my $file1 (@file1) {
	if($file1 =~ m/splic/) {
	push (@matches, $file1); ##loads matches into array @matches
}
}

my @col1; ## column 1
my @col_ID; ## column 2
my @col3; ## column 3
my @col_strand_direction; ## column 6
foreach my $match(@matches) { ## process each line, splitting columns and move onto next line
	my @colsplit = split("\t", $match);
    push (@col3, $colsplit[2] . "\n"); ##pushes third column to @col3 array
	push (@col1, $colsplit[0] . "\n");
	push (@col_ID, $colsplit[1] . "\n");
	push (@col_strand_direction, $colsplit[5] . "\n");
}



my @intron_from_boundary;
my @baseref;


foreach my $col3line(@col3) {
		if ($col3line =~ m/([\+|\-]\d+)\w+(\[[ACTG]])/) { ##pulls out + or - and subsequent number and [base change]
		push (@intron_from_boundary, $1 . "\n"); ##$1 pushes what is in the first set of brackets
		push (@baseref, $2 . "\n");
}
}

## need to take each intronmatch value and work out its position relative to intron/exon boundary

my $left_of_boundary;
my $intron_from_boundary;
my $new_left;
my @spliceout;

## split seq of @col1 into array

my $i = 0;
foreach my $col1(@col1) {
	my @col1split = split(//, $col1);

##for -7:

	 $left_of_boundary = 10; ##10 to the left
	 
		if ($col_strand_direction[$i] =~ m/\+/) {
	 
		$left_of_boundary = $left_of_boundary + $intron_from_boundary[$i]; ##3 to the left

		$new_left = 23 - $left_of_boundary; ## 20
		

		}
		
				else {
		
		$left_of_boundary = $left_of_boundary - $intron_from_boundary[$i]; ##3 to the left

		$new_left = 23 - $left_of_boundary; ## 20
		
		}

		my @spliceout = splice @col1split, $new_left, 22; ##want to pull out 3 letters to left of [G] and 16 to the right }

print "@spliceout\n";
		
			open (MYFILE, '>>fasta');
			print MYFILE (">" . "$col_ID[$i]" , "@spliceout" , "\n");	
			close (MYFILE);
	
	++$i; 
	}